Journal ArticleDOI
Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome
David G. Wang,Jian-Bing Fan,Jian-Bing Fan,Chia-Jen Siao,Chia-Jen Siao,Anthony Berno,Anthony Berno,Peter M. Young,Peter M. Young,Ron Sapolsky,Ron Sapolsky,Ghassan Ghandour,Ghassan Ghandour,Nancy Perkins,Nancy Perkins,Ellen Winchester,Ellen Winchester,Jessica B. Spencer,Jessica B. Spencer,Leonid Kruglyak,Leonid Kruglyak,Lincoln Stein,Lincoln Stein,Linda Hsie,Linda Hsie,Thodoros Topaloglou,Thodoros Topaloglou,Earl Hubbell,Earl Hubbell,Elizabeth M. Robinson,Elizabeth M. Robinson,Michael P. Mittmann,Michael P. Mittmann,Macdonald S. Morris,Macdonald S. Morris,Naiping Shen,Naiping Shen,Dan Kilburn,Dan Kilburn,John D. Rioux,John D. Rioux,Chad Nusbaum,Chad Nusbaum,Steve Rozen,Steve Rozen,Thomas J. Hudson,Thomas J. Hudson,Robert J. Lipshutz,Robert J. Lipshutz,Mark S. Chee,Mark S. Chee,Eric S. Lander,Eric S. Lander +52 more
TLDR
A large-scale survey for SNPs was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips, and a genetic map was constructed showing the location of 2227 candidate SNPs.Abstract:
Single-nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, and they provide powerful tools for a variety of medical genetic studies. In a large-scale survey for SNPs, 2.3 megabases of human genomic DNA was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips. A total of 3241 candidate SNPs were identified. A genetic map was constructed showing the location of 2227 of these SNPs. Prototype genotyping chips were developed that allow simultaneous genotyping of 500 SNPs. The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs.read more
Citations
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Journal ArticleDOI
Recent developments in high-throughput mutation screening.
TL;DR: Methods based on detection using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) have been developed and have a large potential for high-throughput single nucleotide polymorphism (SNP) analysis, due to a very fast analysis time and possibilities for automation.
Journal ArticleDOI
The four faces of Eve: hypothesis compatibility and human origins
John Hawks,Milford H. Wolpoff +1 more
TL;DR: A close examination of the evidence available from four sources, including paleontology, archaeology, the level of human genetic variation, and the geographic structure of human Genetic variation, shows that each of these supports a recent African origin, and no hypothesis of a recent origin is compatible with more than two of them at a time.
Journal ArticleDOI
Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide polymorphism haplotyping.
Jian-Bing Fan,Urvashi Surti,Patricia Taillon-Miller,Linda Hsie,Giulia C. Kennedy,Lori Hoffner,Thomas B. Ryder,David G. Mutch,Pui-Yan Kwok +8 more
TL;DR: The results show that long-range haplotypes can be obtained easily with this resource and that a collection of such samples is a simple way to obtain reference haplotypes for association studies in various populations.
Journal ArticleDOI
Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system
TL;DR: Various genotypes of apolipoprotein E gene were identified from dsDNA obtained by PCR from corresponding patients, and the identity of the DNA base at the SNP site was determined in terms of mass number.
Journal ArticleDOI
Toward a global database for the molecular typing of Saccharomyces cerevisiae strains.
Sandra Jubany,Ivanna H. Tomasco,Inés Ponce de León,Karina Medina,Francisco Carrau,Nicolás Arrambide,Hugo Naya,Carina Gaggero +7 more
TL;DR: In this paper, the authors proposed a standardized methodology for the molecular genotyping of S. cerevisiae strains based on polymorphisms at microsatellite loci and/or single nucleotide polymorphisms (SNPs).
References
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Light-generated oligonucleotide arrays for rapid DNA sequence analysis
Ann Maria Caviani Pease,Dennis W. Solas,Edward Sullivan,Maureen T. Cronin,Christopher P. Holmes,Stephen P. A. Fodor +5 more
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Journal ArticleDOI
An STS-Based Map of the Human Genome
Thomas J. Hudson,Lincoln D. Stein,Sebastian S. Gerety,Junli Ma,Andrew B. Castle,James Silva,Donna K. Slonim,Rafael Baptista,Leonid Kruglyak,Shu-Hua Xu,Xintong Hu,Angela M. E. Colbert,Carl Rosenberg,Mary Pat Reeve-Daly,Steve Rozen,Lester Hui,Xiaoyun Wu,Christina Vestergaard,Kimberly M. Wilson,Jane S. Bae,Shanak Maitra,Soula Ganiatsas,Cheryl A. Evans,Margaret M. DeAngelis,Kimberly A. Ingalls,Robert Nahf,Lloyd T. Horton,Michele Oskin Anderson,Alville Collymore,Wenjuan Ye,Vardouhie Kouyoumjian,Irena S. Zemsteva,James P. Tam,Richard Devine,Dorothy F. Courtney,Michelle Turner Renaud,Huy Nguyen,Tara J. O'Connor,Cécile Fizames,Sabine Fauré,Gabor Gyapay,Colette Dib,Jean Morissette,James B. Orlin,Bruce W. Birren,Nathan Goodman,Jean Weissenbach,Trevor Hawkins,Simon J. Foote,David C. Page,Eric S. Lander +50 more
TL;DR: A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases, anchored by the radiation hybrid and genetic maps.
Journal ArticleDOI
Extensive polymorphisms observed in HIV–1 clade B protease gene using high–density oligonucleotide arrays
Michael J. Kozal,Nila Shah,Naiping Shen,Robert Yang,Raymond V. Fucini,Thomas C. Merigan,Douglas D. Richman,Douglas D. Richman,Don Morris,Earl Hubbell,Mark S. Chee,Thomas R. Gingeras +11 more
TL;DR: In the first clinical application of high–density oligonucleotide arraysequencing, the sequences of 167 viral isolates from 102 patients have been determined and the DNA sequence of USA HIV–1 clade B proteases was found to be extremely variable.
Journal ArticleDOI
Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis.
TL;DR: Fourteen of fifteen patient samples with known mutations were accurately diagnosed, and no false positive mutations were identified in 20 control samples, suggesting DNA chip–based assays may provide a valuable new technology for high–throughput cost–efficient detection of genetic alterations.
Journal ArticleDOI
The use of a genetic map of biallelic markers in linkage studies
TL;DR: How polymorphic and densely spaced biallelic markers need to be for extraction of most of the inheritance information from human pedigrees is examined, and a map of 700–900 moderately polymorphic bialLElic markers is concluded to be equivalent to the current 300–400 microsatellite marker sets.
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